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Transgenic Characterization

From this tab you can browse and select from a list of the reporter lines and driver lines used in the creation of the ALLEN Mouse Brain Connectivity Atlas.


Search the Transgenic Mouse project by entering a gene name, symbol, or mouse line name into the search box. You will be prompted with suggestions once you have started typing. Click "Search" or hit the Enter key.

You can also browse through the data using the browse links on the search page; there are drop-down menus to view all of the #Driver Lines and #Reporter Lines used in this Database.

Driver Lines

Each driver line is represented by it's name, a representative image (which is magnified when clicked on) and a description of expression. Clicking on the line name will return results from all characterization experiments for that particular line.

Reporter Lines

This drop-down menu lists all the characterized reporter lines with a description of their expression patterns.

Search Results

Clicking on Search will return a list of experiments based on your search criteria that outline the Experiment ID, Line Name, Driver, Reporter, Probes, Age, Sex, Treatments and Image Count. Click on the Experiment ID to be taken to the #Experiment Detail Page

To compare multiple experiments, mark the checkboxes to the left of each row, then click the "Compare Selected Experiments" button. Any selections you make will remain selected until you click the "Clear Selections" button.

Experiment Detail Page

Clicking on the experiment summary link returns a summary of the experimental details (see screenshot).

The various sections of the experimental detail page are outlined 1-6 as follows:

  1. Experimental Metadata: Experiment ID, Transgenic Mouse, Driver, Reporter, Related Gene (click for Adult Mouse data), Probes, Plane of Section, Treatments, Induction; Specimen Data: Specimen ID, Organism, Strain, Age, Sex. Related Institute Data
  2. #Image Viewer: Zoom and Pan Viewer
  3. 3-D Thumbnail Viewer: Rotate using the slider bar under the image
  4. Histogram: Relative gene expression in large structures of the brain (for stages older than P28). Hovering your mouse over the histogram will sync the image in the single image viewer with the section corresponding to that structure and expression.
  5. Transgenic Line Metadata: Transgenic lines involved in this experiment including the Type, Name, Stock #, Source (link to Jackson Laboratories), and the Originating Lab.
  6. Probe Information: Probe ID, Type, NCBI Accession, GI, Orientation, Forward Primer, Reverse Primer and Sequence.

Image Viewer

The Zoom and Pan (ZAP) Image Viewer is a powerful tool to navigate and view the images in an experiment. The main part of the viewer is an interactive window where an image can be repositioned by dragging with a mouse. Use the scroll wheel, on-screen navigation buttons or the keyboard to zoom in or out.

Select other images in the experiment by clicking on a thumbnail image below the main viewer.

Scale Bar

Drag the scale bar with your mouse to the desired location. Click the text with your mouse to toggle between horizontal and vertical.

Using the ZAP Viewer Toolbar

Use the toolbar to take actions on the image that currently has focus. Toolbar controls include:



Select ISH, Nissl or Expression image type

Image adjust controls

Display all thumbnail images in a single 'contact sheet'

Open the selected image in the image viewer tool

Keyboard Commands

Use the keyboard to navigate through the image series and synchronize the viewers on the page. Keyboard commands include:




Advance to the next image in the series


Go back to the previous image in the series


Advance to the last image in the series


Go back to the first image in the series


Synchronize all Zap viewers on the page that support synchronization to the currently selected image


Zoom in


Zoom out

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Zoom in. Please note that some keyboards may require the [Shift] key be held down while pressing the [+] key



Zoom out

You can also use the arrow keys to pan the current image.

Expression Energy

The expression mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

The Expression Energy was calculated as follows: Within a given area A (voxel or structure), expression energy = (sum of intensity of expressing pixels in A) / (sum of all pixels in A)

High Resolution Image Viewer

The image viewer enables you to view a high resolution image in its own re-sizable window. It it possible to open multiple images by opening multiple windows.

Ways to interact with an image include:

  • Drag the image with your mouse pointer to an area of interest, then click to zoom in.
  • Drag the red boundary box in the thumbnail window to manipulate the image.
  • Use the Zoom and Pan tools at the bottom of the viewer window to pan to an area of interest and zoom in or out
  • Use the toolbar tabs menu at the bottom-left of the window to view a different image from the same series, or to retrieve additional information.

Using the Toolbar Tabs Menu

The Toolbar Tabs Menu can be expanded or hidden by clicking the arrow in the top right-hand corner. The following table describes the function of each option in the various tabs of the toolbar:



Navigate the images in this experiment

Choose between ISH, Nissl or Expression Image views

Change the contrast of the current image by using the slider bar, or by manually entering in a value between 0-100. Click "Reset" to go back to the default setting.

Email or Download the current image, or show keyboard commands

Using the Toolbar



Launch a High Resolution Image Viewer

Launch a contact sheet viewer

Pan left

Pan up

Pan down

Pan right

View fluorescent image (for fluorescent experiments only)

View ISH image (for ISH experiments only)

View #expression mask (for ISH experiments only)

View the nearest Nissl

Reset image defaults

Image Adjustment

Dark field images, such as fluorescent proteins (XFP), double fluorescent ISH (DFISH) & some immunohistochemistry (IHC) can be enhanced one color-channel at a time. To the right of each color slider control is the name of the probe expressed in that channel. The center position is neutral (image is neither enhanced nor diminished in that channel). Move the slider to the right to enhance the color, and to the left to diminish the color.

Bright-field images, such as colorimetric ISH and Nissl stained images have a single contrast slider control. Center is neutral, right is brighter, left is darker.

Experiment Metadata

Much of the background for each experiment is contained in the metadata panel. Where applicable, there are hyperlinks to the web site of the transgenic mouse distributor for further information on the mouse lines represented in the experiment. In most cases, there is also a link to the Allen Brain Atlas for the driver gene.

Clicking on the Related Data link will return a list of other Allen Institute projects using that particular gene.

Applicable probe details will be made visible by clicking on the "Show Probe Details" bar at the bottom of the metadata panel.

Expression Mask

The Expression mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

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